rs3851059

Variant names:

• chr10-80270902-G-A
• rs3851059

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.277 in 152,092 control chromosomes in the GnomAD database, including 6,054 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6054 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42148 AN: 151974 Hom.: 6047 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.272

Gnomad ASJ AF: 0.285

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.273

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.277 AC: 42174 AN: 152092 Hom.: 6054 Cov.: 32 AF XY: 0.282 AC XY: 20949 AN XY: 74348

African (AFR) AF: 0.205 AC: 8495 AN: 41482

American (AMR) AF: 0.272 AC: 4165 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.285 AC: 988 AN: 3472

East Asian (EAS) AF: 0.435 AC: 2253 AN: 5178

South Asian (SAS) AF: 0.363 AC: 1748 AN: 4816

European-Finnish (FIN) AF: 0.312 AC: 3297 AN: 10566

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20247 AN: 67972

Other (OTH) AF: 0.273 AC: 577 AN: 2112

Alfa AF: 0.291 Hom.: 21500

Bravo AF: 0.271

Asia WGS AF: 0.384 AC: 1332 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.2
DANN	Benign	0.42
PhyloP100		0.036

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3851059; hg19: chr10-82030658;